If you will return in the future I would not suggest trying to squeeze in Seoul. I don't know how helpful it would be in regards to acclimatisation. I would rather spend the time and money to add that extra time in Vietnam. I am not sure what your flight is like prior to arrival in Seoul but I am assuming it will be long. I would be tired after the flight. Are you planning on checking into your hotel first to rest a bit and then going out sightseeing? You don't have two full days and if you factor in the time spent clearing customs, another hour minimum getting to and from Seoul, the time spent sleeping and the time allowed to check in it takes away at least 14 hours. If this was the only chance to see the city I would go for it but IMO Seoul isn't the kind of city that you want to see again and again. My son lives there and I visited there about three years ago. The only reason I want to go back is to see him!

We did what you are proposing a few years back but only for one overnight in Seoul. Very much worth it. We did a full day tour to the DMZ which has become one of our top travel experiences. Don't let the naysayers discourage you.

DO IT!
I have taken these flights to Vietnam and if you have time, a short layover in Seoul would be worth it. See if you can get an "early check-in" at a hotel. Or if you want to do the DMZ, get a hotel in Incheon, dump your stuff and take the subway or train to Seoul for your tour. The DMZ tour starts at about 7-8am and you would finish about 3pm. Granted, a long day, but if you can sleep on the flight over, you should be ok. If you stay in Incheon, you would be close for your continuation flight.
Or....get a hotel in Seoul....take a short rest and head out to see the Palaces, head to the markets, or just experience Seoul for a short time.

I say do the stop. I am going to both North and South Korea in September. From what I can learn, South Korea is a rapidly changing society - right now a combination of new and old. Even if you do get back in 5 - 10 years, it may have changed quite a bit in that amount of time. You can get some kind of "feel" for a place even in a day and a half just wandering around. Take the fastest bus or train you can find into Seoul. A DMZ tour would take much of the day, so you would need to decide if that is more important than just soaking up the city. Also, there are some tours from the airport for people with long layovers. Check with the tourist office about those.

I'm planning on a holiday in seoul. what is the estimated budget required if I depart from malaysia? Which hotel should I stay? can you recommend places in seoul? thank you

One word of caution - be conscious of the temperature differences between vn and Korean. We almost made the mistake of going to Korea in feb/march, when the temperature would have been hot in vn, but frigid in korea. If you are going, be sure to take the proper clothing.